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crisprBwa

This is the development version of crisprBwa; for the stable release version, see crisprBwa.

BWA-based alignment of CRISPR gRNA spacer sequences

Bioconductor version: Development (3.18)

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

Author: Jean-Philippe Fortin [aut, cre]

Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>

Citation (from within R, enter citation("crisprBwa")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("crisprBwa")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crisprBwa")
Introduction to crisprBwa HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, CRISPR, FunctionalGenomics, Software
Version 1.5.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends methods
Imports BiocGenerics, BSgenome, crisprBase(>= 0.99.15), GenomeInfoDb, Rbwa, readr, stats, stringr, utils
Linking To
Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat
System Requirements
Enhances
URL https://github.com/crisprVerse/crisprBwa
Bug Reports https://github.com/crisprVerse/crisprBwa/issues
See More
Depends On Me
Imports Me
Suggests Me crisprDesign
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package crisprBwa_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64) crisprBwa_1.5.0.tgz
macOS Binary (arm64) crisprBwa_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/crisprBwa
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/crisprBwa
Bioc Package Browser https://code.bioconductor.org/browse/crisprBwa/
Package Short Url https://bioconductor.org/packages/crisprBwa/
Package Downloads Report Download Stats